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- PDB-4b6c: Structure of the M. smegmatis GyrB ATPase domain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4b6c
TitleStructure of the M. smegmatis GyrB ATPase domain in complex with an aminopyrazinamide
ComponentsDNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit B
KeywordsISOMERASE / DNA TOPOISOMERASE / INHIBITOR
Function / homology
Function and homology information


DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII ...DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-B5U / DNA gyrase subunit B
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTucker, J.A. / Shirude, P.S. / Madhavapeddi, P. / Hussein, S. / Basu, R. / Ghorpade, S.
CitationJournal: ACS Chem. Biol. / Year: 2013
Title: Aminopyrazinamides: novel and specific GyrB inhibitors that kill replicating and nonreplicating Mycobacterium tuberculosis.
Authors: Shirude, P.S. / Madhavapeddi, P. / Tucker, J.A. / Murugan, K. / Patil, V. / Basavarajappa, H. / Raichurkar, A.V. / Humnabadkar, V. / Hussein, S. / Sharma, S. / Ramya, V.K. / Narayan, C.B. / ...Authors: Shirude, P.S. / Madhavapeddi, P. / Tucker, J.A. / Murugan, K. / Patil, V. / Basavarajappa, H. / Raichurkar, A.V. / Humnabadkar, V. / Hussein, S. / Sharma, S. / Ramya, V.K. / Narayan, C.B. / Balganesh, T.S. / Sambandamurthy, V.K.
History
DepositionAug 9, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references / Structure summary
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Nov 28, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / entity_src_nat / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_fragment / _entity.pdbx_mutation / _entity.src_method / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit B
B: DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9836
Polymers43,9872
Non-polymers9954
Water2,018112
1
A: DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4913
Polymers21,9941
Non-polymers4982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4913
Polymers21,9941
Non-polymers4982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.455, 82.251, 191.941
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.5585, 0.82947, 0.00742), (0.8295, 0.5585, 0.00276), (-0.00186, 0.0077, -0.99997)
Vector: -19.27874, -16.43661, 142.69847)

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Components

#1: Protein DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit B


Mass: 21993.738 Da / Num. of mol.: 2
Fragment: ATPASE DOMAIN, RESIDUES 9-102,123-213,246-255,ATPASE DOMAIN, RESIDUES 9-102,123-213,246-255,ATPASE DOMAIN, RESIDUES 9-102,123-213,246-255
Mutation: YES,YES,YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Gene: gyrB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0C559, EC: 5.99.1.3
#2: Chemical ChemComp-B5U / 6-(3,4-dimethylphenyl)-3-[[4-[3-(4-methylpiperazin-1-yl)propoxy]phenyl]amino]pyrazine-2-carboxamide


Mass: 474.598 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H34N6O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 103-122 DELETED AND RESIDUES 213-246 REPLACED BY DG TO IMPROVE CRYTALLISABILITY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.54 % / Description: NONE
Crystal growpH: 5.7
Details: 100MM NA ACETATE PH 5.7, 200MM CALCIUM ACETATE, 19% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 29, 2009 / Details: VARIMAXHF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→28.06 Å / Num. obs: 16117 / % possible obs: 89.8 % / Observed criterion σ(I): 2 / Redundancy: 5.26 % / Biso Wilson estimate: 38.64 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 5.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.64 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.3 / % possible all: 51.9

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: INTERNAL MSM GYRB MODEL

Resolution: 2.2→28.06 Å / Cor.coef. Fo:Fc: 0.9374 / Cor.coef. Fo:Fc free: 0.9228 / SU R Cruickshank DPI: 0.338 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.353 / SU Rfree Blow DPI: 0.24 / SU Rfree Cruickshank DPI: 0.24
RfactorNum. reflection% reflectionSelection details
Rfree0.2539 815 5.06 %RANDOM
Rwork0.199 ---
obs0.2017 16098 89.74 %-
Displacement parametersBiso mean: 40.05 Å2
Baniso -1Baniso -2Baniso -3
1-3.7341 Å20 Å20 Å2
2---6.8215 Å20 Å2
3---3.0874 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 72 112 2754
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012723HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.073699HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d924SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes68HARMONIC2
X-RAY DIFFRACTIONt_gen_planes403HARMONIC5
X-RAY DIFFRACTIONt_it2723HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion17.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion342SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3135SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.35 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2748 115 6.12 %
Rwork0.1981 1764 -
all0.203 1879 -
obs--89.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.744-0.32150.70692.4743-0.26422.5775-0.00620.05120.03280.10340.0254-0.0890.1220.23-0.01920.0562-0.0060.02940.163-0.0162-0.005521.940940.674782.3372
22.65910.01570.56471.158-1.03021.9857-0.11070.00130.08260.01220.0587-0.0127-0.0908-0.0320.0520.02540.02140.00830.0802-0.0209-0.02191.683524.464760.5549
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESIDUES 36 - 255
2X-RAY DIFFRACTION2CHAIN B AND RESIDUES 37 - 255

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